Base de dados : MEDLINE
Pesquisa : D12.776 [Categoria DeCS]
Referências encontradas : 177635 [refinar]
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[PMID]:29414979
[Au] Autor:Takahashi H; Kozhuharova A; Sharma H; Hirose M; Ohyama T; Fasolo F; Yamazaki T; Cotella D; Santoro C; Zucchelli S; Gustincich S; Carninci P
[Ad] Endereço:RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan.
[Ti] Título:Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation.
[So] Source:PLoS One;13(2):e0183229, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:SINEUPs are antisense long noncoding RNAs, in which an embedded SINE B2 element UP-regulates translation of partially overlapping target sense mRNAs. SINEUPs contain two functional domains. First, the binding domain (BD) is located in the region antisense to the target, providing specific targeting to the overlapping mRNA. Second, the inverted SINE B2 represents the effector domain (ED) and enhances translation. To adapt SINEUP technology to a broader number of targets, we took advantage of a high-throughput, semi-automated imaging system to optimize synthetic SINEUP BD and ED design in HEK293T cell lines. Using SINEUP-GFP as a model SINEUP, we extensively screened variants of the BD to map features needed for optimal design. We found that most active SINEUPs overlap an AUG-Kozak sequence. Moreover, we report our screening of the inverted SINE B2 sequence to identify active sub-domains and map the length of the minimal active ED. Our synthetic SINEUP-GFP screening of both BDs and EDs constitutes a broad test with flexible applications to any target gene of interest.
[Mh] Termos MeSH primário: Biossíntese de Proteínas/genética
Proteínas/genética
RNA Longo não Codificante/genética
[Mh] Termos MeSH secundário: Animais
Linhagem Celular Tumoral
Células HEK293
Seres Humanos
Camundongos
Fosforilação
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Proteins); 0 (RNA, Long Noncoding)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180208
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0183229


  2 / 177635 MEDLINE  
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[PMID]:28456785
[Au] Autor:Huang H; Wang Y; Chen H; Chen Y; Wu J; Chiang PW; Fan N; Su Y; Deng J; Chen D; Li Y; Zhang X; Zhang M; Liang S; Banerjee S; Qi M; Liu X
[Ad] Endereço:BGI-Shenzhen, Shenzhen, China.
[Ti] Título:Targeted next generation sequencing identified novel mutations in RPGRIP1 associated with both retinitis pigmentosa and Leber's congenital amaurosis in unrelated Chinese patients.
[So] Source:Oncotarget;8(21):35176-35183, 2017 May 23.
[Is] ISSN:1949-2553
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:As the most common inherited retinal degenerations, retinitis pigmentosa (RP) is clinically and genetically heterogeneous. Some of the RP genes are also associated with other retinal diseases, such as LCA (Leber's congenital amaurosis) and CORD (cone-rod dystrophy). Here, in our molecular diagnosis of 99 Chinese RP patients using targeted gene capture sequencing, three probands were found to carry mutations of RPGRIP1, which was known to be associated with pathogenesis of LCA and CORD. By further clinical analysis, two probands were confirmed to be RP patients and one was confirmed to be LCA patient. These novel mutations were co-segregated with the disease phenotype in their families. Our result not only expands the mutational spectrum of the RPGRIP1 gene but also gives supports to clinical diagnosis and molecular treatment of RP patients.
[Mh] Termos MeSH primário: Grupo com Ancestrais do Continente Asiático/genética
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Amaurose Congênita de Leber/genética
Mutação
Proteínas/genética
Retinite Pigmentosa/genética
[Mh] Termos MeSH secundário: Adulto
China
Feminino
Estudos de Associação Genética
Predisposição Genética para Doença
Seres Humanos
Masculino
Linhagem
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteins); 0 (RPGRIP1 protein, human)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170501
[St] Status:MEDLINE
[do] DOI:10.18632/oncotarget.17052


  3 / 177635 MEDLINE  
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[PMID]:28456689
[Au] Autor:Mandic A; Strebinger D; Regali C; Phillips NE; Suter DM
[Ad] Endereço:The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland.
[Ti] Título:A novel method for quantitative measurements of gene expression in single living cells.
[So] Source:Methods;120:65-75, 2017 May 01.
[Is] ISSN:1095-9130
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Gene expression is at the heart of virtually any biological process, and its deregulation is at the source of numerous pathological conditions. While impressive progress has been made in genome-wide measurements of mRNA and protein expression levels, it is still challenging to obtain highly quantitative measurements in single living cells. Here we describe a novel approach based on internal tagging of endogenous proteins with a reporter allowing luminescence and fluorescence time-lapse microscopy. Using luminescence microscopy, fluctuations of protein expression levels can be monitored in single living cells with high sensitivity and temporal resolution over extended time periods. The integrated protein decay reporter allows measuring protein degradation rates in the absence of protein synthesis inhibitors, and in combination with absolute protein levels allows determining absolute amounts of proteins synthesized over the cell cycle. Finally, the internal tag can be excised by inducible expression of Cre recombinase, which enables to estimate endogenous mRNA half-lives. Our method thus opens new avenues in quantitative analysis of gene expression in single living cells.
[Mh] Termos MeSH primário: Imagem Molecular/métodos
Proteínas/genética
Análise de Célula Única/métodos
Coloração e Rotulagem/métodos
Transcrição Genética
[Mh] Termos MeSH secundário: Animais
Linhagem Celular
Genes Reporter/genética
Vetores Genéticos/genética
Meia-Vida
Integrases/genética
Lentivirus/genética
Luminescência
Camundongos
Microscopia de Fluorescência/métodos
Imagem Molecular/instrumentação
Proteínas/química
Proteínas/metabolismo
Proteólise
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Análise de Célula Única/instrumentação
Coloração e Rotulagem/instrumentação
Imagem com Lapso de Tempo/instrumentação
Imagem com Lapso de Tempo/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteins); 0 (RNA, Messenger); EC 2.7.7.- (Cre recombinase); EC 2.7.7.- (Integrases)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170501
[St] Status:MEDLINE


  4 / 177635 MEDLINE  
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[PMID]:29282749
[Au] Autor:Hou L; Wang J; Wang Y; Hua X; Wu J
[Ad] Endereço:Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), School of Medicine, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.
[Ti] Título:Compared proteomic analysis of 8- and 32-week-old postnatal porcine ovaries.
[So] Source:Cell Biochem Funct;36(1):34-42, 2018 Jan.
[Is] ISSN:1099-0844
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Pigs share many anatomical and physiological features with humans, offering a unique and viable model for biomedical research. Tandem mass tag method followed by mass spectrometry analysis was utilized to identify peptides (47,405), proteins (14,701), and protein groups (7634) in ovaries of 8- and 32-week-old postnatal Banna miniature pigs. After annotation and analysis by Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology, the proteins were identified as being involved in hormone metabolic pathways and maintenance, proliferation, and regulation of stem cells. In addition, we found 638 differentially expressed proteins between ovaries of 8- and 32-week-old postnatal Banna miniature pigs. We used Interactive Pathway Explorer to produce an overview of pig ovarian proteomics. Compared with those of the 8-week-old group, the proteins enriched in metabolism of steroid hormones, metabolism of lipids, and energy metabolism pathway were upregulated in the 32-week-old group, indicating physiological characteristics of sexual maturity. These findings have implications in applications of biomedicine. SIGNIFICANCE OF THE STUDY: Pigs share many anatomical and physiological features with humans, offering a unique and viable model for biomedical research. In this study, we used tandem mass tag quantitative proteomics to describe, for the first time, protein expression patterns of postnatal pig ovaries. Proteins involved in hormone metabolic pathways and maintenance, proliferation, and regulation of stem cells were identified. With further analysis by Interactive Pathway Explorer, proteins enriched in metabolism of steroid hormones, metabolism of lipids, and energy metabolism pathway were upregulated in the 32-week-old group, indicating physiological characteristics of sexual maturity. These findings have implications in applications of biomedicine.
[Mh] Termos MeSH primário: Ovário/química
Peptídeos/análise
Proteínas/análise
Proteômica
[Mh] Termos MeSH secundário: Animais
Proliferação Celular
Cromatografia Líquida
Feminino
Espectrometria de Massas
Camundongos
Camundongos Nus
Ovário/metabolismo
Peptídeos/metabolismo
Proteínas/metabolismo
Células-Tronco/citologia
Células-Tronco/metabolismo
Suínos
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Peptides); 0 (Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171229
[St] Status:MEDLINE
[do] DOI:10.1002/cbf.3315


  5 / 177635 MEDLINE  
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[PMID]:29270670
[Au] Autor:Lv C; Wang H; Tong Y; Yin H; Wang D; Yan Z; Liang Y; Wu D; Su Q
[Ad] Endereço:Department of General Surgery, Shengjing Hospital Affiliated to China Medical University, Shenyang City, Liaoning Province, 110004, People's Republic of China.
[Ti] Título:The function of BTG3 in colorectal cancer cells and its possible signaling pathway.
[So] Source:J Cancer Res Clin Oncol;144(2):295-308, 2018 Feb.
[Is] ISSN:1432-1335
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:PURPOSE: B-cell translocation gene 3 (BTG3) has been identified as a candidate driver gene for various cancers, but its specific role in colorectal cancer (CRC) is poorly understood. We aimed to investigate the relationship between expression of BTG3 and clinicopathological features and prognosis, as well as to explore the effects and the role of a possible BTG3 molecular mechanism on aggressive colorectal cancer behavior. METHODS: BTG3 expression was assessed by immunohistochemistry (IHC) on specimens from 140 patients with CRC. The association of BTG3 expression with clinicopathological features was examined. To confirm the biological role of BTG3 in CRC, two CRC cell lines expressing BTG3 were used and BTG3 expression was knocked down by shRNA. CCK-8, cell cycle, apoptosis, migration, and invasion assays were performed. The influence of BTG3 knockdown was further investigated by genomic microarray to uncover the potential molecular mechanisms underlying BTG3-mediated CRC development and progression. RESULTS: BTG3 was downregulated in colorectal cancer tissues and positively correlated with pathological classification (p = 0.037), depth of invasion (p = 0.016), distant metastasis (p = 0.024), TNM stage (p = 0.007), and overall survival (OS) and disease-free survival (DFS). BTG3 knockdown promoted cell proliferation, migration, invasion, relieved G2 arrest, and inhibited apoptosis in HCT116 and LoVo cells. A genomic microarray analysis showed that numerous tumor-associated signaling pathways and oncogenes were altered by BTG3 knockdown. At the mRNA level, nine genes referred to the extracellular-regulated kinase/mitogen-activated protein kinase pathway were differentially expressed. Western blotting revealed that BTG3 knockdown upregulated PAK2, RPS6KA5, YWHAB, and signal transducer and activator of transcription (STAT)3 protein levels, but downregulated RAP1A, DUSP6, and STAT1 protein expression, which was consistent with the genomic microarray data. CONCLUSIONS: BTG3 expression might contribute to CRC carcinogenesis. BTG3 knockdown might strengthen the aggressive colorectal cancer behavior.
[Mh] Termos MeSH primário: Neoplasias Colorretais/metabolismo
Proteínas/metabolismo
[Mh] Termos MeSH secundário: Linhagem Celular Tumoral
Movimento Celular/fisiologia
Proliferação Celular/fisiologia
Neoplasias Colorretais/genética
Neoplasias Colorretais/patologia
Regulação para Baixo
Feminino
Técnicas de Silenciamento de Genes
Células HCT116
Células HT29
Seres Humanos
Imuno-Histoquímica
Masculino
Meia-Idade
Inclusão em Parafina
Proteínas/genética
Transdução de Sinais
Células Tumorais Cultivadas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (BTG3 protein, human); 0 (Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171223
[St] Status:MEDLINE
[do] DOI:10.1007/s00432-017-2561-9


  6 / 177635 MEDLINE  
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[PMID]:29244012
[Au] Autor:Jelínek J; Skoda P; Hoksza D
[Ad] Endereço:Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, Czech Republic. jelinek@ksi.mff.cuni.cz.
[Ti] Título:Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.
[So] Source:BMC Bioinformatics;18(Suppl 15):492, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. RESULTS: We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank. All proteins involved in PPIs were converted into labeled graphs with nodes corresponding to amino acids and edges to pairs of neighboring amino acids. A structural neighborhood of each node was then encoded into a bit string and stored in the knowledge base. When predicting PPIs, INSPiRE labels amino acids of unknown proteins as interface or non-interface based on how often their structural neighborhood appears as interface or non-interface in the knowledge base. We evaluated INSPiRE's behavior with respect to different types and sizes of the structural neighborhood. Furthermore, we examined the suitability of several different features for labeling the nodes. Our evaluations showed that INSPiRE clearly outperforms existing methods with respect to Matthews correlation coefficient. CONCLUSION: In this paper we introduce a new knowledge-based method for identification of protein-protein interaction sites called INSPiRE. Its knowledge base utilizes structural patterns of known interaction sites in the Protein Data Bank which are then used for PPI prediction. Extensive experiments on several well-established datasets show that INSPiRE significantly surpasses existing PPI approaches.
[Mh] Termos MeSH primário: Aminoácidos
Bases de Conhecimento
Mapeamento de Interação de Proteínas/métodos
Proteínas
Software
[Mh] Termos MeSH secundário: Aminoácidos/química
Aminoácidos/metabolismo
Biologia Computacional
Bases de Dados de Proteínas
Modelos Estatísticos
Proteínas/química
Proteínas/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Amino Acids); 0 (Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1921-4


  7 / 177635 MEDLINE  
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[PMID]:29244007
[Au] Autor:Haspel N; Luo D; González E
[Ad] Endereço:Department of Computer Science, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, 02125, MA, USA. nurit.haspel@umb.edu.
[Ti] Título:Detecting intermediate protein conformations using algebraic topology.
[So] Source:BMC Bioinformatics;18(Suppl 15):502, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Understanding protein structure and dynamics is essential for understanding their function. This is a challenging task due to the high complexity of the conformational landscapes of proteins and their rugged energy levels. In particular, it is important to detect highly populated regions which could correspond to intermediate structures or local minima. RESULTS: We present a hierarchical clustering and algebraic topology based method that detects regions of interest in protein conformational space. The method is based on several techniques. We use coarse grained protein conformational search, efficient robust dimensionality reduction and topological analysis via persistent homology as the main tools. We use two dimensionality reduction methods as well, robust Principal Component Analysis (PCA) and Isomap, to generate a reduced representation of the data while preserving most of the variance in the data. CONCLUSIONS: Our hierarchical clustering method was able to produce compact, well separated clusters for all the tested examples.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Conformação Proteica
Proteínas
[Mh] Termos MeSH secundário: Análise por Conglomerados
Análise de Componente Principal
Proteínas/química
Proteínas/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1918-z


  8 / 177635 MEDLINE  
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[PMID]:29188662
[Au] Autor:Ren GH; Weng RH; Shi Y; Huang P; Deng KF; Liu NG; Chen YJ
[Ad] Endereço:Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Science, Ministry of Justice, P.R.China, Shanghai 200063, China.
[Ti] Título:[Analysis of Differentially Expressed Proteins Distribution in the Rat Brains with DAI by MALDI-TOF-IMS].
[So] Source:Fa Yi Xue Za Zhi;32(4):241-244, 2016 Aug.
[Is] ISSN:1004-5619
[Cp] País de publicação:China
[La] Idioma:chi
[Ab] Resumo:OBJECTIVES: To establish the imaging mass spectrometry for analysis of differentially expressed proteins distribution in the rat brains with diffuse axonal injury (DAI) based on matrix assisted laser desorption/ionization-time of flight imaging mass spectrometry (MALDI-TOF-IMS). METHODS: MALDI-TOF-IMS scanning were conducted on the brains of DAI group and control group in the range of 1 000 to 20 000 using AutoflexⅢ MALDI-TOF spectrometer. ClinProTool 2.2 software was used for statistical analysis on the data of two groups, and then the differentially expressed proteins were picked out to conduct imaging. The distribution of the proteins with different in the rat brains was observed. RESULTS: Five proteins with different , including 4 963, 5 634, 6 253, 6 714 and 7 532, differentially expressed in the rat brains with DAI. CONCLUSIONS: MALDI-TOF-IMS can be used for studying the differentially expressed proteins in rat brains with DAI and the analysis method is established for exploring the distribution of differentially expressed proteins in the rat brains with DAI using imaging mass spectrometry.
[Mh] Termos MeSH primário: Encéfalo/metabolismo
Lesão Axonal Difusa/metabolismo
Proteínas/metabolismo
Proteoma/metabolismo
[Mh] Termos MeSH secundário: Animais
Encéfalo/patologia
Lesão Axonal Difusa/patologia
Proteômica
Ratos
Software
Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteins); 0 (Proteome)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171201
[St] Status:MEDLINE
[do] DOI:10.3969/j.issn.1004-5619.2016.04.001


  9 / 177635 MEDLINE  
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[PMID]:29221443
[Au] Autor:Yao Y; Gui R; Liu Q; Yi M; Deng H
[Ad] Endereço:Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, 430070, China.
[Ti] Título:Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction.
[So] Source:BMC Bioinformatics;18(1):542, 2017 Dec 08.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: As one of the most successful knowledge-based energy functions, the distance-dependent atom-pair potential is widely used in all aspects of protein structure prediction, including conformational search, model refinement, and model assessment. During the last two decades, great efforts have been made to improve the reference state of the potential, while other factors that also strongly affect the performance of the potential have been relatively less investigated. RESULTS: Based on different distance cutoffs (from 5 to 22 Å) and residue intervals (from 0 to 15) as well as six different reference states, we constructed a series of distance-dependent atom-pair potentials and tested them on several groups of structural decoy sets collected from diverse sources. A comprehensive investigation has been performed to clarify the effects of distance cutoff and residue interval on the potential's performance. Our results provide a new perspective as well as a practical guidance for optimizing distance-dependent statistical potentials. CONCLUSIONS: The optimal distance cutoff and residue interval are highly related with the reference state that the potential is based on, the measurements of the potential's performance, and the decoy sets that the potential is applied to. The performance of distance-dependent statistical potential can be significantly improved when the best statistical parameters for the specific application environment are adopted.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Conformação Proteica
Proteínas/química
Proteínas/ultraestrutura
[Mh] Termos MeSH secundário: Bases de Conhecimento
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171210
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1983-3


  10 / 177635 MEDLINE  
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[PMID]:29187139
[Au] Autor:Calyseva J; Vihinen M
[Ad] Endereço:Protein Structure and Bioinformatics, Department of Experimental Medical Science, Lund University, BMC B13, SE-22 184, Lund, Sweden.
[Ti] Título:PON-SC - program for identifying steric clashes caused by amino acid substitutions.
[So] Source:BMC Bioinformatics;18(1):531, 2017 Nov 29.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Amino acid substitutions due to DNA nucleotide replacements are frequently disease-causing because of affecting functionally important sites. If the substituting amino acid does not fit into the protein, it causes structural alterations that are often harmful. Clashes of amino acids cause local or global structural changes. Testing structural compatibility of variations has been difficult due to the lack of a dedicated method that could handle vast amounts of variation data produced by next generation sequencing technologies. RESULTS: We developed a method, PON-SC, for detecting protein structural clashes due to amino acid substitutions. The method utilizes side chain rotamer library and tests whether any of the common rotamers can be fitted into the protein structure. The tool was tested both with variants that cause and do not cause clashes and found to have accuracy of 0.71 over five test datasets. CONCLUSIONS: We developed a fast method for residue side chain clash detection. The method provides in addition to the prediction also visualization of the variant in three dimensional structure.
[Mh] Termos MeSH primário: Aminoácidos/química
Proteínas/química
Software
[Mh] Termos MeSH secundário: Algoritmos
Substituição de Aminoácidos
Aminoácidos/metabolismo
Bases de Dados de Proteínas
Conformação Proteica
Engenharia de Proteínas/métodos
Proteínas/genética
Proteínas/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Amino Acids); 0 (Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171201
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1947-7



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